[med-svn] r1860 - in trunk/packages/clustalw/trunk: . debian debian/patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Wed May 14 00:10:34 UTC 2008
Author: plessy
Date: 2008-05-14 00:10:33 +0000 (Wed, 14 May 2008)
New Revision: 1860
Removed:
trunk/packages/clustalw/trunk/debian/patches/bug_119_gpp4.3-autoptr.patch
Modified:
trunk/packages/clustalw/trunk/CHANGELOG
trunk/packages/clustalw/trunk/debian/changelog
trunk/packages/clustalw/trunk/debian/clustalw.1
trunk/packages/clustalw/trunk/debian/clustalw.1.xml
trunk/packages/clustalw/trunk/debian/copyright
Log:
New upstream release.
Modified: trunk/packages/clustalw/trunk/CHANGELOG
===================================================================
--- trunk/packages/clustalw/trunk/CHANGELOG 2008-05-13 03:50:13 UTC (rev 1859)
+++ trunk/packages/clustalw/trunk/CHANGELOG 2008-05-14 00:10:33 UTC (rev 1860)
@@ -1,4 +1,31 @@
----------------------------------------------------------------------
+Version 2.0.7
+----------------------------------------------------------------------
+
+* Fixed bug 121: CRLF in sequence names (Pearson) are not trimmed
+
+* Fixed bug 122: convert option broken
+
+* Fixed reopened bug 114: profile alignment input didn't work with new
+ getSeqRange routines
+
+* Fixed bug 119: build with g++ 4.3
+
+----------------------------------------------------------------------
+Version 2.0.6
+----------------------------------------------------------------------
+
+* Fixed bug 77: fasta input performance issue
+
+* Fixed bug 114: segfault while doing profile alignment with secondary
+ structure mask
+
+* Removed unncessary id console output in EMBLFileParser.cpp
+
+* Fixed Bugs 108 and 109 and allowed mixed-case command line options
+
+
+----------------------------------------------------------------------
Version 2.0.5
----------------------------------------------------------------------
Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog 2008-05-13 03:50:13 UTC (rev 1859)
+++ trunk/packages/clustalw/trunk/debian/changelog 2008-05-14 00:10:33 UTC (rev 1860)
@@ -1,3 +1,18 @@
+clustalw (2.0.7-1) unstable; urgency=low
+
+ * New upstream release.
+ - Fixes bug 121: CRLF in sequence names (Pearson) are not trimmed.
+ - Fixes bug 122: convert option broken.
+ - Fixes reopened bug 114: profile alignment input didn't work with new
+ getSeqRange routines.
+ - Fixes bug 119: build with g++ 4.3.
+ * Removed debian/patches/bug_119_gpp4.3-autoptr.patch, obsoleted by the
+ above correction.
+ * Incremented version number in debian/clustalw.1*
+ * Uptated debian/copyright to the latest draft of the format.
+
+ -- Charles Plessy <plessy at debian.org> Wed, 14 May 2008 09:07:26 +0900
+
clustalw (2.0.6-1) unstable; urgency=low
[Charles Plessy]
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1 2008-05-13 03:50:13 UTC (rev 1859)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1 2008-05-14 00:10:33 UTC (rev 1860)
@@ -1,11 +1,11 @@
.\" Title: CLUSTALW
.\" Author: Des Higgins
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 05/01/2008
+.\" Date: 05/14/2008
.\" Manual: Clustal Manual
-.\" Source: Clustal 2.0.6
+.\" Source: Clustal 2.0.7
.\"
-.TH "CLUSTALW" "1" "05/01/2008" "Clustal 2.0.6" "Clustal Manual"
+.TH "CLUSTALW" "1" "05/14/2008" "Clustal 2.0.7" "Clustal Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-05-13 03:50:13 UTC (rev 1859)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml 2008-05-14 00:10:33 UTC (rev 1860)
@@ -18,7 +18,7 @@
<!ENTITY dhsurname "Plessy">
<!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "2.0.6">
+ <!ENTITY dhrelease "2.0.7">
<!ENTITY dhtitle "Clustal Manual">
<!ENTITY dhucpackage "CLUSTALW">
<!ENTITY dhpackage "clustalw">
Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright 2008-05-13 03:50:13 UTC (rev 1859)
+++ trunk/packages/clustalw/trunk/debian/copyright 2008-05-14 00:10:33 UTC (rev 1860)
@@ -1,34 +1,12 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
-X-Debianized-Date: Fri, 28 Aug 1998 16:09:48 +0200
-X-Source-Downloaded-From: http://www.clustal.org/download/current/
-X-Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: Stephane Bortzmeyer <bortzmeyer at debian.org>
+Debianized-Date: Fri, 28 Aug 1998 16:09:48 +0200
+Original-Source-Location: http://www.clustal.org/download/current/clustalw-2.0.7-src.tar.gz
+Upstream-Author: Des Higgins, Julie Thompson and Toby Gibson
X-Non-Free-Autobuild: yes
The licence does not forbid Debian from using autobuilders to create binary
packages.
-Files: debian/*
-Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
- © 2001 Dr. Guenter Bechly <gbechly at debian.org>
- © 2001 Adrian Bunk <bunk at fs.tum.de>
- © 2001-2002 Andreas Tille <tille at debian.org>
- © 2006 Kai Hendry <hendry at iki.fi>
- © 2007 Nelson A. de Oliveira <naoliv at debian.org>
- © 2003-2008 Steffen Möller <moeller at debian.org>
- © 2007-2008 Charles Plessy <plessy at debian.org>
- © 2008 David Paleino <d.paleino at gmail.com>
-Licence: Unclear
- The licence of the earlier works was never stated. Some works have been
- obsoleted by release of version 2.0 — the lesstif migration for instance —
- but authors are left in the list of copyright holders by courtesy. The work
- of Charles Plessy and Steffen Möller can be treated as if it were public domain.
-
-Files: debian/clustalw.1.xml, debian/clustalw.1
-Copyright: © 2008 Charles Plessy <plessy at debian.org>
-Licence: Public Domain
- The manual page and its XML source can be used, modified, and
- redistributed as if it were in public domain.
-
Files: *
Copyright: © Des Higgins, Julie Thompson and Toby Gibson
Licence: Not for commercial use, No modification of the code.
@@ -88,3 +66,25 @@
those modifications do not alter the algorithmic core, i.e. only affect
installation routines, bug fixes etc. Please include the original
LICENSE file into your package."
+
+Files: debian/*
+Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
+ © 2001 Dr. Guenter Bechly <gbechly at debian.org>
+ © 2001 Adrian Bunk <bunk at fs.tum.de>
+ © 2001-2002 Andreas Tille <tille at debian.org>
+ © 2006 Kai Hendry <hendry at iki.fi>
+ © 2007 Nelson A. de Oliveira <naoliv at debian.org>
+ © 2003-2008 Steffen Möller <moeller at debian.org>
+ © 2007-2008 Charles Plessy <plessy at debian.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+Licence: Unclear
+ The licence of the earlier works was never stated. Some works have been
+ obsoleted by release of version 2.0 — the lesstif migration for instance —
+ but authors are left in the list of copyright holders by courtesy. The work
+ of Charles Plessy and Steffen Möller can be treated as if it were public domain.
+
+Files: debian/clustalw.1.xml, debian/clustalw.1
+Copyright: © 2008 Charles Plessy <plessy at debian.org>
+Licence: Public Domain
+ The manual page and its XML source can be used, modified, and
+ redistributed as if it were in public domain.
Deleted: trunk/packages/clustalw/trunk/debian/patches/bug_119_gpp4.3-autoptr.patch
===================================================================
--- trunk/packages/clustalw/trunk/debian/patches/bug_119_gpp4.3-autoptr.patch 2008-05-13 03:50:13 UTC (rev 1859)
+++ trunk/packages/clustalw/trunk/debian/patches/bug_119_gpp4.3-autoptr.patch 2008-05-14 00:10:33 UTC (rev 1860)
@@ -1,24 +0,0 @@
-Index: src/tree/UPGMA/UPGMAAlgorithm.h
-===================================================================
---- src/tree/UPGMA/UPGMAAlgorithm.h (revision 178)
-+++ src/tree/UPGMA/UPGMAAlgorithm.h (working copy)
-@@ -7,6 +7,7 @@
- #include "../AlignmentSteps.h"
- #include "RootedGuideTree.h"
- #include <list>
-+#include <memory>
-
- namespace clustalw
- {
-Index: src/tree/UPGMA/Node.h
-===================================================================
---- src/tree/UPGMA/Node.h (revision 178)
-+++ src/tree/UPGMA/Node.h (working copy)
-@@ -2,6 +2,7 @@
- #define _NODE_H
- #include <limits>
- #include <vector>
-+#include <string>
- #include "upgmadata.h"
- namespace clustalw
- {
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